Polyketides are natural products produced by a wide range of organisms, and particularly by microorganisms. Polyketides have many important pharmaceutical, veterinary and agricultural uses. Polyketides encompass a huge range of chemical structural space, and have a wide range of associated biological activities. Polyketides with use in medical treatments include antibiotics, immunosuppressants, antitumor agents, other chemotherapeutic agents, and other compounds possessing a broad range of therapeutic and biological properties. The Gram-positive bacteria Streptomyces and their allied genera are prodigious producers of polyketides, and the genetics and biochemistry of polyketide biosynthesis in these organisms are relatively well characterised (Hopwood, 1997). The genes for polyketide biosynthesis in Streptomyces are clustered and the exploitation of DNA technology has made it possible to isolate complete biosynthetic gene clusters by screening gene libraries with DNA probes encoding the genes responsible for their biosynthesis. Thus, increasing numbers of gene clusters for polyketide biosynthesis in Streptomyces and other microorganisms have been isolated and sequenced, including, for example, those for the polyether monensin (WO 01/68867), the polyene nystatin (WO 01/59126) and for rapamycin (Schwecke et al., 1995).
Polyketides are synthesised through the repeated condensation of building blocks that contain a carboxylic acid function. At each stage of the process this results in the formation of a new β-keto function and an α-side chain branch into the growing chain. The structural diversity of polyketides derives from a number of aspects of their biosynthetic pathway including: the wide variety of starter units that may be utilised in their biosynthesis; the different lengths of polyketide chains that are possible; the various α-side chains that are introduced either during or after assembly of the polyketide chain; the various β-substitutions that may be introduced during or after assembly of the polyketide chain; the various degrees of processing that the β-keto groups can undergo (keto, hydroxyl, enoyl, and methylene); and the various stereochemistries that are possible at the α- and β-centres.
The synthesis of polyketides is catalysed by an enzyme, or by a complex of enzymes, called the polyketide synthase (PKS) in a manner similar to that of fatty acid biosynthesis. Streptomyces and related genera PKSs fall into three main categories: type-I, type-II and type-III. The type-III PKSs are small proteins related to plant chalcone synthases that have been discovered only recently (Moore & Hopke, 2000). Type-III systems have been implicated in the biosynthesis of a small number of secondary metabolites but may be more generally involved in the biosynthesis of soluble pigments (Cortés et al., 2002). The type-II PKSs consist of several monofunctional proteins that act as a multi-polypeptide complex. Simple aromatic polyketides such as actinorhodin are formed by several rounds of chain assembly, which are performed iteratively on one set of type-II PKS enzymes that are encoded for by one set of PKS genes (Hopwood, 1997). Type-I PKSs are multifunctional proteins and are required for the synthesis of more complex polyketides such as erythromycin and rapamycin. As the focus of this patent, type-I PKS organisation and function are described in detail below:
Type-I PKSs are organised into modules, whereby each module consists of several catalytic ‘domains’ that are required to carry out one round of chain assembly (Staunton & Wilkinson, 1997). In general a modular PKS contains the correct number of modules (loading plus extension modules) to select and condense the correct number of loading and extension units. For example the erythromycin PKS consists of 7 modules (one loading and six extension modules) to select and condense the one starter and six extension units required for the biosynthesis of the erythromycin precursor 6-deoxyerythronolide B. Thus, there exists a one to one relationship between the number of modules present in the PKS and the number of units incorporated. This one to one relationship is described as ‘co-linearity’.
The term ‘extension module’ as used herein refers to the set of contiguous domains, from the β-ketoacyl-acyl carrier protein synthase (KS) domain to the next acyl carrier protein (ACP) domain, which accomplishes one cycle of polyketide chain extension. The term ‘loading module’ as used herein refers to any group of contiguous domains that accomplishes the loading of the starter unit onto the PKS and thus renders it available to the KS domain of the first extension module. Besides condensation of the next extender carboxylic acid (or ketide) unit onto the growing polyketide chain, which is performed by the catalytic activity of the essential KS domain, modules of type-I PKSs may contain domains with β-ketoreductase (KR), dehydratase (DH), and enoyl reductase (ER) activities which are responsible for the further processing of the newly formed β-keto groups during chain extension. The acyl transferase (AT) and the ACP domains present in each module are responsible for the choice of extender unit, and the tethering of the growing chain during its passage on the PKS respectively. The AT domains of a modular PKS can also be found as discrete proteins (Cheng et al., 2003). The completed polyketide chain is generally released from PKSs by the action of a terminal thioesterase (TE) domain that is also generally involved in the cyclisation (lactonisation) of the final product. Other chain terminating/cyclising strategies are also employed such as that for the addition of an amino acid residue and macrolactam formation as observed for rapamycin (Schwecke et al., 1995), for macrolactam formation as for rifamycin (August et al., 1998), and for amino acid incorporation followed by reductive elimination as for myxalamid biosynthesis (Silakowski et al., 2001). In summary, there is a single enzymatic domain present for each successive catalytic step that occurs during biosynthesis on the PKS, and they are used in defined sequence that depends upon their location within the protein and the particular function they perform. This mechanism is termed ‘processive’.
The modular arrangement of type-I PKSs was first confirmed by mutation of the erythromycin PKS (also known as 6-deoxyerythronolide B synthase, DEBS) through an in-frame deletion of a region of the KR domain of module 5 (Donadio et al., 1991). This led to the production of the erythromycin analogues, 5,6-dideoxy-3-α-mycarosyl-5-oxoerythronolide B and 5,6-dideoxy-5-oxoerythronolide B, due to the inability of the mutated KR domain to reduce the β-keto group 5 at this stage of processive biosynthesis. Likewise, alteration of the active site residues in the ER domain of module 4 of DEBS2, by genetic engineering of the corresponding PKS-encoding DNA and its introduction into Saccharopolyspora erythraea, led to the production of 6,7-anhydroerythromycin C (Donadio et al., 1993). In addition, the length of the polyketide chain formed by DEBS has been altered through the specific relocation of the TE domain of DEBS3 to the end of DEBS1; the expected triketide lactone product was produced in good yield (Cortés et al., 1995). It should be noted that the changes described involved modification by deletion of sequence, or by sequence specific inactivation, or by the alternative juxtaposition of DNA sequence from within the same PKS cluster (ie. they are considered ‘homologous changes’). Other such ‘homologous’ changes to the erythromycin PKS are described in WO 93/13663.
The modular organisation of type-I PKS genes lends itself to the manipulation of these genes to produce altered polyketide structures. Type I PKSs represent an assembly line for polyketide biosynthesis that can be manipulated by changing the number of modules; by changing their specificities towards different carboxylic acid starter units and extender units; by inactivating, mutating, removing, swapping or inserting domains with different activities and specificities; and by altering the chain or ring size through the repositioning of termination or cyclisation domains (Staunton & Wilkinson, 1997).
WO 98/01546 describes the production of hybrid PKS gene assemblies comprising the incorporation of heterologous DNA. WO 98/01546 describes methods for generating hybrid PKSs in which the substitution of genes encoding heterologous modules, sub-modules or domains for the native genes generates novel polyketides with altered structures. Specifically, for example the AT domains of heterologous DNA from the rapamycin or monensin PKSs can be exchanged for that native to the erythromycin PKS in order to generate novel polyketides with altered alkyl branching. Such an AT domain swap represented the first example of the production of a truly hybrid PKS (Oliynyk et al., 1996). WO 98/01546 also describes in general terms the production of hybrid PKS assemblies comprising a loading module and at least one extension module. It specifically describes the construction of a hybrid PKS gene assembly by grafting the broad-specificity loading module for the avermectin-producing PKS onto the first protein of the erythromycin PKS (DEBS1) in place of the normal loading module (see also Marsden et al., 1998). Additional examples comprising loading module swaps that are substrate specific have also been described (WO 00/00618; U.S. Pat. No. 5,876,991; Kuhstoss et al., 1996). WO 00/01827 describes methods for varying the β-keto processing capability of a PKS module through the ability to swap ‘reductive loops’, ie. the ability to rapidly and in a combinatorial manner, alter the number and type of ketoreductase, dehydratase and enoyl reductase domains within a module. In addition to changing the level of β-keto group processing, such changes may also lead to changes in stereochemistry of the α-alkyl and β-hydroxyl groups thus formed by the altered modules.
Although modular PKSs operate ‘normally’ in a co-linear and processive manner as described above, examples of a deviation from this mode of operation have been described and are discussed below.
The picromycin PKS gene cluster in Streptomyces venezuelae is responsible for the biosynthesis of both picromycin (a 14-membered, heptaketide macrolide) and methymycin (a 12-membered, hexaketide macrolide) (Xue et al., 1998). The ability of a single PKS to produce two related macrolides, of different ring sizes, derives from the alternative expression of the final PKS gene pikA4 (Xue & Sherman, 2000). When ‘normal’ expression occurs and full-length PikA4 is formed, a sixth extension unit is incorporated and the picromycin aglycone is produced; when alternative expression occurs and an N-terminally truncated form of PikA4 is produced, no sixth extension unit is incorporated and the growing polyketide chain is passed directly to the TE domain which leads to formation of the methymycin aglycone. Thus, a breakdown of co-linearity occurs and a ‘ring contracted’ product is formed. The biochemical basis for this phenomenon has been investigated and shown to be an ACP5 to ACP6 transfer, missing out covalent attachment to the intervening KS6 domain; such a breakdown of co-linearity has been called ‘skipping’ (Beck et al., 2002).
Skipping has also been observed to occur when an extra extension module from the rapamycin PKS was interpolated into the erythromycin PKS in order to convert the natural heptketide-producing PKS Into an octaketide-producing one (Rowe et al., 2001). The expected octaketide, 16-membered macrolide was produced, but the major product was the normal heptaketide product 6-deoxyerythronolide. This ‘skipping’ of the interpolated module is believed to occur due to the interpolated module acting on some occasions as a ‘shuttle’, passing the growing chain from the preceding module to the following downstream module without performing a round of chain extension. It was subsequently shown that the ACP domain of the interpolated module is essential in passing the growing polyketide chain from the preceding ACP domain and passing it to the KS domain of the following module during skipping (Thomas et al., 2002), a mechanism similar to that described for methymycin biosynthesis above. It is shown that skipping can occur without the active site nucleophile of the KS domain. A ring-contracted (skipped) nemadectin (an antiparasitic macrolide) has been reported from a mutant of a Streptomyces soil isolate that was modified by chemical mutation (Rudd et al., 1990); the biosynthesis of the natural PKS product was abolished.
An alternative manner in which modular PKSs deviate from co-linear operation involves the iterative operation of modules. For example, module 4 of the erythromycin PKS appears to operate iteratively, at a low level, to produce a ring expanded 16-membered, octaketide macrolide related to 6-deoxyerythronolide B (Wilkinson et al., 2000). The ability of the erythromycin PKS to perform this operation has been termed ‘stuttering’. The ‘stuttering’ of the erythromycin PKS is considered an aberrant process, as the products of this stuttering are formed in low yield and the major product of the erythromycin PKS is the normal heptaketide 6-deoxyerythonolide B formed by co-linear operation. Products that appear to be formed by both stuttering and skipping have also been reported as minor components from the epothilone producer Sorangium cellulosum (Hardt et al., 2001). The stigmatellin biosynthetic cluster of Stigmatella aurantiaca encodes for a PKS that comprises ten (one loading and nine extension) modules (Gaitatzis et al., 2002); however, based on results from structural elucidation and the feeding of stable isotope labelled substrates, stigmatellin is formed from eleven modular derived units. Thus, it would appear that one of the stigmatellin PKS modules operates (twice) iteratively.
Since the priority filing of the present application, the sequence of the PKS responsible for biosynthesis of the macrolide lankacidin by Streptomyces rochei has been described (Mochizuki et al., 2003). This PKS also appears to contain too few modules in comparison to the number of extension cycles required for lankacidin biosynthesis, although the mechanism by which this would occur is not clear.
Additional structural diversity can be generated through the modification of polyketides by enzymes other than the PKS, either during the process of chain assembly as seen during the biosynthesis of some ansamycins (Floss, 2001), or after the process of chain assembly following release from the PKS. Such non-PKS mediated reactions may include, but are not limited to the following: reduction, oxidation, hydroxylation, acylation, alkylation, amination, decarboxylation, dehydration, double bond isomerisation/migration, cyclisation, ring cleavage, conjugation, glycosylation, reductive elimination and any combination of these. When these reactions occur after chain assembly they are termed the post-PKS or tailoring steps. Such tailoring steps are generally, but not always, essential for endowing the polyketide natural product with biological activity.
In addition, the structural diversity of polyketides obtainable biosynthetically can be further enhanced through the use of defined heterologous post-PKS tailoring enzymes as well as through the use of those which naturally modify the natural polyketide (Gaisser et al., 2000). WO 01/79520 describes the heterologous modification of polyketide macrolide structures through glycosylation, epoxidation, hydroxylation, and methylation. The ability to generate analogues of the agricultural compound spinosyn through glycosylation with alternative deoxyhexose substituents has been reported (Gaisser et al., 2002).
Borrelidin 1 (FIG. 1) is an 18-membered macrolide produced by several bacterial strains including, but not limited to, Streptomyces rochei ATCC23956, Streptomyces parvulus Tü113 and Streptomyces parvulus Tü4055. Borrelidin is herein shown to be derived from a trans-cyclopentane-1,2-dicarboxylic acid starter acid, three malonyl-CoA and five methylmalonyl-CoA extender units (see FIG. 2). From the absolute stereochemistry of borrelidin, based on the crystal structure and recently confirmed through total synthesis, the actual starter acid is predicted to be trans-cyclopentane-(1R,2R)-dicarboxylic acid. Borrelidin isolated after the feeding of stable isotope labelled acetate and propionate substrates clearly indicated the expected incorporation of these building blocks; in addition, it has been demonstrated in the present application that feeding of trans-cyclopentane-1,2-dicarboxylic acid was sufficient to re-establish borrelidin biosynthesis in mutants where specific genes believed to be involved in the formation of the starter unit had been disrupted. Borrelidin contains a nitrile group attached to the C12 position, which is shown herein to arise through the action of tailoring enzymes acting upon a methylmalonyl-CoA derived methyl branch present at this position. The gross structure of borrelidin was first elucidated in 1967 (Keller-Scheirlein, 1967), and was subsequently refined by detailed NMR analysis (Kuo et al., 1989). The absolute configuration of borrelidin was confirmed by X-ray crystallography (Anderson et al., 1989). Its co-identity as the antibiotic treponemycin has been verified (Maehr & Evans, 1987).
A number of groups have reported the synthesis of fragments of the borrelidin structure, and since the priority filing of the present application, two independent total syntheses of borrelidin have been reported (Hanessian et al., 2003; Duffey et al., 2003).
Borrelidin was first discovered due to its antibacterial activity (Berger et al., 1949), although this antibacterial activity extends only to a limited number of micrococci, and is not found against all common test bacteria. The mode of action in sensitive microorganisms involves selective inhibition of threonyl tRNA synthetase (Paetz & Nass, 1973). Other activities against spirochetes of the genus Treponema (Singh et al., 1985; U.S. Pat. No. 4,759,928), against viruses (Dickinson et al., 1965), uses for the control of animal pests and weeds (DE 3607287) and use as an agricultural fungicide (DE 19835669; U.S. Pat. No. 6,193,964) have been reported. Additionally, since the priority filing of the present application, borrelidin has been reported to have antimalarial activity against drug resistant Plasmodium falciparum strains (Otoguro et al., 2003). Between all of these reports only two reported any synthetically modified derivatives. The first of these describes the benzyl ester and its bis-O-(4-nitrobenzoyl) derivative (Berger et al., 1949). The second of these describes the borrelidin methyl ester, the methyl ester bis O-acetyl derivative, and the methyl ester Δ14-15-dihydro-, Δ14-15,12-13-tetrahydro-, and Δ14-15,12-13-tetrahydro-C12-amino derivatives (Anderton & Rickards, 1965). No biological activity was reported for any of these compounds.
A recent disclosure of particular interest is the discovery that borrelidin displays anti-angiogenesis activity (Wakabayashi et al., 1997). Angiogenesis is the process of the formation of new blood vessels. Angiogenesis occurs only locally and transiently in adults, being involved in, for example, repair following local trauma and the female reproductive cycle. It has been established as a key component in several pathogenic processes including cancer, rheumatoid arthritis and diabetic retinopathy. Its importance in enabling tumours to grow beyond a diameter of 1-2 cm was established by Folkman (Folkman, 1986), and is provoked by the tumour responding to hypoxia. In its downstream consequences angiogenesis is mostly a host-derived process, thus inhibition of angiogenesis offers significant potential in the treatment of cancers, avoiding the hurdles of other anticancer therapeutic modalities such as the diversity of cancer types and drug resistance (Matter, 2001). It is of additional interest that recent publications have described the functional involvement of tyrosinyl- and tryptophanyl tRNA synthetases in the regulation of angiogenesis (Wakasugi et al., 2002; Otani et al., 2002).
In the rat aorta matrix culture model of angiogenesis, borrelidin exhibits a potent angiogenesis-inhibiting effect and also causes disruption of formed capillary tubes in a dose dependent manner by inducing apoptosis of the capillary-forming cells (Wakabayashi et al., 1997). Borrelidin inhibited capillary tube formation with an IC50 value of 0.4 ng/ml (0.8 nM). In the same study, borrelidin was shown to possess anti-proliferative activity towards human umbilical vein endothelial cells (HUVEC) in a cell growth assay; the IC50 value was measured at 6 ng/ml, which is 15-fold weaker than the anti-angiogenesis activity measured in the same medium. This anti-proliferative activity of borrelidin was shown to be general towards various cell lines. In addition to these data the authors report that borrelidin inhibits tRNA synthetase and protein synthesis in the cultured rat cells; however the IC50 value for anti-angiogenesis activity (0.4 ng/ml) was 50-fold lower than that reported for inhibition of protein synthesis (20 ng/ml), indicating different activities of the compound.
Borrelidin also displays potent inhibition of angiogenesis in vivo using the mouse dorsal air sac model (Funahashi et al., 1999), which examines VEGF-induced angiogenesis and is an excellent model for studying tumour-angiogenesis. Borrelidin was administered at a dose of 1.8 mg/kg by intraperitoneal injection and shown to significantly reduce the increment of vascular volume induced by WiDr cells, and to a higher degree than does TNP-470, which is a synthetic angiogenesis inhibitor in clinical trials. Detailed controls verified that these data are for angiogenesis inhibition and not inhibition of growth of the tumour cells. The authors also showed that borrelidin is effective for the inhibition of the formation of spontaneous lung metastases of B16-BL6 melanoma cells at the same dosage by inhibiting the angiogenic processes involved in their formation.
JP 9-227,549 and JP 8-173,167 confirm that borrelidin is effective against WiDr cell lines of human colon cancer, and also against PC-3 cell lines of human prostate cancer. JP 9-227,549 describes the production of borrelidin by Streptomyces rochei Mer-N7167 (Ferm P-14670) and its isolation from the resulting fermentation culture. In addition to borrelidin 1,12-desnitrile-12-carboxyl borrelidin 2 (presumably a biosynthetic intermediate or shunt metabolite), 10-desmethyl borrelidin 3 (presumably a biosynthetic analogue arising from the mis-incorporation of an alternative malonyl-CoA extender unit in module 4 of the borrelidin PKS), 11-epiborrelidin 4 and the C14,C15-cis borrelidin analogue 5 were described (see FIG. 1). Thus, JP 9-227,549 specifies borrelidin and borrelidin analogues wherein a nitrile or carboxyl group is attached the carbon skeleton at C12, and a hydrogen atom or lower alkyl group is attached to the carbon skeleton at C10.
WO 01/09113 discloses the preparation of borrelidin analogues that have undergone synthetic modification at the carboxylic acid moiety of the cyclopentane ring. The activity of these compounds was examined using endothelial cell proliferation and endothelial capillary formation assays In a similar manner to that described above. In general, modification of the carboxyl moiety improved the selectivity for inhibiting capillary formation: the major reason for this improvement in selectivity is through a decrease in the cell proliferation inhibition activity whereas the capillary formation inhibitory activity was altered to a much lower degree. Specifically, the borrelidin-morpholinoethyl ester showed a 60-fold selectivity index, the borrelidin-amide showed a 37-fold selectivity index, the borrelidin-(2-pyridyl)-ethyl ester showed a 7.5-fold selectivity index and the borrelidin-morpholinoethyl amide showed a 6-fold selectivity index, for the capillary formation inhibitory activity versus cell proliferation with respect to borrelidin. The capillary formation inhibitory activity of these and other borrelidin derivatives was verified using a micro-vessel formation assay. In addition, the authors showed that borrelidin weakly inhibited the propagation of metastatic nodules, after removal of the primary tumour, when using a Lewis lung adenocarcinoma model. However, the borrelidin-(3-picolylamide) derivative was reported to inhibit very considerably the increase of micrometastases in rats after intraperitoneal and also with per os administration at subtoxic doses. Similarly, using the colon 38 spleen liver model, the metastasis-forming ability of mouse colon adenocarcinoma cells transplanted into mouse spleen was considerably decreased after treatment with a subtoxic dose of this borrelidin derivative. These data confirm the earlier reported ability of borrelidin and its derivatives to inhibit the formation of metastases.
Borrelidin has also been identified as an inhibitor of cyclin-dependant kinase Cdc28/Cln2 of Saccharomyces cerivisiae with an IC50 value of 12 μg/ml (24 μM) (Tsuchiya et al., 2001). It was shown that borrelidin arrests both haploid and diploid cells in late G1 phase (at a time point indistinguishable from α-mating pheromone), and at concentrations that do not affect gross protein biosynthesis. These data were taken to indicate that borrelidin has potential as a lead compound to develop anti-tumour agents.
Since the priority filing of the present application, two further reports have been published concerning the biological activity of borrelidin. The first of these indicates that the anti-angiogenic effects of borrelidin are mediated through distinct pathways (Kawamura et al., 2003). High concentrations of threonine were found to attenuate the ability of borrelidin to inhibit both capillary tube formation in the rat aorta culture model and HUVEC cells proliferation; however, it did not affect the ability of borrelidin to collapse formed capillary tubes or to induce apoptosis in HUVEC. Borrelidin was also found to activate caspase-3 and caspase-8, and inhibitors of both of these suppressed borrelidin induced apoptosis in HUVEC. The second of these papers used the method of global cellular mRNA profiling to provide insight into the effects of borrelidin on Saccharomyces cerevisiae (Eastwood and Schaus, 2003). This analysis showed the induction of amino acid biosynthetic enzymes in a time-dependent fashion upon treatment with borrelidin, and it was ascertained that the induction of this pathway involves the GCN4 transcription factor.
In summary, the angiogenesis-inhibitory effect of borrelidin is directed towards the twin tumour-biological effects of proliferation and capillary formation. In addition, borrelidin, and derivatives thereof, have been shown to inhibit the propagation of metastases. Borrelidin also has indications for use in cell cycle modulation. Thus, borrelidin and related compounds are particularly attractive targets for investigation as therapeutic agents for the treatment of tumour tissues, either as single agents or for use as an adjunct to other therapies. In addition, they may be used for treating other diseases in which angiogenesis is implicated in the pathogenic process, including, but not restricted to, the following list: rheumatoid arthritis, psoriasis, atherosclerosis, diabetic retinopathy and various ophthalmic disorders.